Dear Khaleel,
The pattern should be written as "^(?:(?!T{5,}).)+ $", which means not containing 5 consecutive Ts in any region of the gRNA.
Please try
biocLite("CRISPRseek") with the quotation, which worked for me.
It would be great if you could post this on https://support.bioconductor.org . Many thanks!
Best regards,
Julie
On May 16, 2016, at 4:10 AM, Khaleel Rababah <krababah@yahoo.com> wrote:
Hi Dr.Zhu,
I was reading your paper CRISPRseek, i tried to understand the gRNA pattern in CRISPRseek that you mentioned in your paper: gRNA.pattern=‘‘‘(?:(?!T{5,}).)+ $". my question is what the pattern is really
Second thing is, i tried to install CRISPRSEEK but i could not, the following is what i did:
source("http://bioconductor.org/biocLite.R") Installing package into ‘C:/Users/Um Tarq/Documents/R/win-library/3.2’ (as ‘lib’ is unspecified) trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/BiocInstaller_1.20.3.zip' Content type 'application/zip' length 57033 bytes (55 KB) downloaded 55 KB
biocLite() BioC_mirror: https://bioconductor.orgUsing Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.5 (2016-04-14). Old packages: 'cluster', 'Matrix', 'nlme', 'survival' Update all/some/none? [a/s/n]: a Warning in install.packages(update[instlib == l, "Package"], l, repos = repos, : 'lib = "C:/Program Files/R/R-3.2.5/library"' is not writable trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/cluster_2.0.4.zip'Content type 'application/zip' length 530785 bytes (518 KB) downloaded 518 KB trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/Matrix_1.2-6.zip'Content type 'application/zip' length 3645108 bytes (3.5 MB) downloaded 3.5 MB trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/nlme_3.1-128.zip'Content type 'application/zip' length 2143924 bytes (2.0 MB) downloaded 2.0 MB trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/survival_2.39-4.zip'Content type 'application/zip' length 4816804 bytes (4.6 MB) downloaded 4.6 MB package ‘cluster’ successfully unpacked and MD5 sums checked package ‘Matrix’ successfully unpacked and MD5 sums checked package ‘nlme’ successfully unpacked and MD5 sums checked package ‘survival’ successfully unpacked and MD5 sums checked
biocLite(CRISPRseek) Error in match(x, table, nomatch = 0L) : object 'CRISPRseek' not found
Also i am trying to install biocLite(CRISPRseek) but i get
Error in match(x, table, nomatch = 0L) : object 'CRISPRseek' not found Your help is appreciated